Pontine and forebrain cholinergic nuclei contribute to the regulation of breathing and arousal. This report summarizes experiments in rat (n = 20) concerning the cholinergic interaction between pons and basal forebrain. In vitro [(35)S]guanylyl-5'-O-(gamma-thio)-triphosphate ([(35)S]GTPgammaS) autoradiography quantified carbachol-stimulated guanine nucleotide binding (G) protein activation in seven basal forebrain nuclei. Carbachol significantly increased [(35)S]GTPgammaS binding in the vertical and horizontal limbs of the diagonal band of Broca, medial and lateral septum, and nucleus basalis (B)/substantia innominata (SI). In vitro receptor autoradiography demonstrated muscarinic receptors in the same nuclei where carbachol caused G protein activation. In vivo experiments showed that carbachol administered to the pontine reticular formation (PnO) significantly decreased the number of 7-14Hz spindles in the electroencephalogram (EEG), decreased acetylcholine release in SI, and decreased respiratory rate. Carbachol microinjection into SI did not alter the number of EEG spindles or respiratory rate. The results help clarify that EEG and rate of breathing are more effectively modulated by cholinergic neurotransmission in PnO than in SI.